[Objectives]  To reveal the genetic structure and diversity of 13 geographical populations of Conopomorpha sinensis in China by analyzing variation in the COⅠgene fragment. [Methods]  COⅠ gene fragments of 258 C. sinensis specimens from 13 geographical populations were amplified using PCR and sequenced. Based on the sequences obtained, haplotype composition, genetic diversity and genetic differentiation, of the geographic populations were analyzed with bioinformatic methods. [Results]  The length of the COⅠ gene fragment amplified from the 258 specimens was 1 349 bp. 56 haplotypes were identified, including 14 common haplotypes and 42 population-specific haplotypes, which indicates a relatively high level of gene flow and genetic differentiation among geographic populations. Haplotype 4 is a common haplotype among all 13 geographical populations, indicating that it is relatively primitive, adaptable and stable in C. sinensis. Genetic diversity analysis indicates that geographical populations of C. sinensis have high haplotype diversity (F_st) and low nucleotide diversity (N_m). The fixed coefficient (F_st) and gene flow (N_m) for all specimens were 0.085 and 5.382, respectively, indicating a high level of gene flow among populations. [Conclusion]  There is evidence of frequent gene exchange between different geographical populations of C. sinensis. The total population may have experienced rapid growth in the past, but there has been insufficient time to accumulate nucleotide mutations, resulting in a relatively high level of haplotype diversity, but a low level of nucleotide diversity.